It isn’t everyday that a sauropod vertebra makes it onto the cover of a technical journal. In fact… this might be the first time that it’s ever happened (please let us know if you know otherwise. So far as I can tell, even Journal of Vertebrate Paleontology has never had a sauropod vertebra on the cover [though it has featured sauropod skeletons in their entirety]). Yes world, I give you the cover of issue 1 of Volume 31 of Cretaceous Research, a journal I do editing work for. We’ve had dinosaurs on the cover before (a Triceratops skull), but when the opportunity arose for new submissions I decided to try my luck. I submitted a nice photo of MIWG.7306 (aka ‘Angloposeidon’) – albeit it only the posterior half – and… here we are. This is a major achievement, it’s open-bar night here at SV-POW!

PS – Mike and I tried to get a sauropod vertebra on a journal cover back in 2007. We failed. Can you guess what that particular sauropod vertebra was?

Advertisements

7306 anterior half in section

Inspired by Mike’s recent post on the interior of Chondrosteosaurus from the Isle of Wight’s Wessex Formation, what could I do but weigh in yet again with one of my most-loved specimens: the beauty that is MIWG.7306 (aka ‘Angloposeidon’), a big brachiosaurid also from the Wessex Formation (Naish et al. 2004). As mentioned previously, it’s perhaps intuitively surprising that one of the most useful things about MIWG.7306 is that it’s broken in two, allowing us to see the broken faces of both halves of the vertebra. This allows us to see the internal structure of the specimen and, potentially, to work out, not just what the internal architecture was like, but also how pneumatic this beast was. To date Matt and I have done some preliminary work on this, but we have yet to publish anything, so what you’re getting here is a world first, never-before-seen by anyone outside.. well, me and Matt. In fact I can’t recall whether even Mike has seen this stuff: IT’S THAT SECRET.

Anyway, what we’re looking at here is the posterior broken face of the anterior half of MIWG.7306. The specimen was photographed lying on its side but I’ve reoriented the photo such that the dorsal surface is at the top, of course. The broken surface looks at first sight like a big mess, mostly obscured by sediment which has gotten preserved within the pneumatic spaces. However, it you look carefully you’ll see very dark (blackish) spars of bone scattered about the interior. These are the thin bony walls that surround the internal cavities, called camellae, that made up the vertebra’s interior. Much of the ventral part of the cross-section is taken up by the vertical median septum: much of the space lateral to the septum (on both its left and right sides) would have been occupied by large air sacs. I was hoping to use a fully labelled version of this photo but cleverly seem to have lost it (and don’t have time to knock up a new version). For the full details you’ll have to wait for the paper!

7306 section, ventral part

Ventral to the median septum, the vertebra is again wide when seen in cross-section, and in the photo here we’re looking at that ventral part, though this time we’re looking at the anterior face of the posterior half of the vertebra. What’s nice is that there are clearly at least four distinct camellae aligned along the centrum’s ventral edge, and they don’t appear to be equal in size (nor arranged symmetrically around the midline). The actual ventral floor of the centrum can also be clearly seen in cross-section, and it’s pretty thin. All of this is particularly interesting because we have comparative data from North American brachiosaurids (in particular from a specimen that Matt has scanned, BYU 12866) and from Sauroposeidon (Wedel et al. 2000a, b). ‘Angloposeidon’ is similar enough to both of these in its details to convince us that the same sort of thing is going on, but it’s also different in various subtle ways: the ventral floor of the centrum is not the same thickness in all of these animals for example.

In the article on Chondrosteosaurus, Mike noted that we can work out how much of a vertebra’s interior was occupied by air if we can calculate the bone : air space ratio. We did just this with MIWG.7306, using the photos shown here and several others. The result: MIWG.7306 approached Sauroposeidon in terms of its pneumaticity, being 80-90% air. This gives us some remarkable and significant data on the palaeobiology of this animal, as pneumaticity has all sorts of implications for the animal’s respiration, physiology and mass (Wedel 2003, 2005). And on that note, I shall say goodbye.

References

Sauroposeidon in 3D

April 18, 2014

Sauroposeidon meet Sauroposeidon

I was in Oklahoma and Texas last week, seeing Sauroposeidon, Paluxysaurus, Astrophocaudia, and Alamosaurus, at the Sam Noble Oklahoma Museum of Natural History, the Fort Worth Museum of Science and History, the Shuler Museum of Paleontology at SMU, and the Perot Museum of Nature and Science, respectively. I have a ton of interesting things from that trip that I could blog about, but unfortunately I have no time. Ten days from now, I’m off to Colorado and Utah for the Mid-Mesozoic conference and field trip, and between now and then I need to finish up my bits on three collaborative papers, get my summer anatomy lectures posted for internal peer review here at WesternU, and–oh yeah–actually write my conference talk. Fun times.

BUT after being subjected to the horror of the Yale Brontosaurus skull, I figured you all deserved a little awesome.

Photographing Sauroposeidon 2014-04-07

So here’s me getting one of 351 photos of the most posterior and largest of the Sauroposeidon jackets (this is not the awesome, BTW, just a stop along the way). This jacket holds what I once inferred to be the back half of C7 and all of C8. Now that Sauroposeidon may be a somphospondyl rather than a brachiosaur, who knows what verts these are–basal somphospondyls have up to 17 cervicals to brachiosaurids’ probable 13 (for a hypothetical view of an even-longer-necked Sauroposeidon, see this probably-prophetic post by Mike). The vertically-mounted skeleton in the background is Cotylorhynchus. Cotylorhynchus got a lot bigger than that–up to maybe 6 meters long and 2 or 3 tons–and was probably the largest land animal that had ever existed back in the Early Permian. Photo by OU grad student Andrew Thomas, whom you’ll be hearing about more here in the future.

I couldn’t crank the model myself on the road, thanks to the pathetic lack of processing power in my 6-year-old laptop (which will be replaced RSN). Andy Farke volunteered to do the photogrammetricizing with Agisoft Photoscan, if only I’d DropBox him the pictures. Here’s a screenshot from MeshLab showing the result:

Sauroposeidon lateral PLY 10 - 6 and 9 blended

And my best taken-from-overhead quasi-lateral photograph:

Sauroposeidon C8 jacket lateral photo 2014-04-07

If you’re curious, the meter stick at the top is actually one meter long, it just has the English measurement side showing. The giant caliper at the bottom is also marked off in inches, and it is open to 36.0 inches (it didn’t go to 1 meter, or I would have used that). You can tell that there is some perspective distortion involved here since 36 inches on the caliper is 1380 pixels, whereas the 39.4-inch meter stick is only 1341 pixels. Man, I hate scale bars. But they make good calibration targets.

Incidentally, after playing around with the model in orthographic mode in MeshLab, the distortions in the photos of the vertebrae themselves just scream at me. Finally, finally, I can escape the tyranny of perspective. Compare the ends of the big wooden beam at the top of the jacket to get a feel for how much the two views differ.

Working on Sauroposeidon again after all this time made me seriously nostalgic. I love that beast. I don’t think I’m exaggerating when I say that those vertebrae are the most gorgeous physical objects in the universe. Also, an appropriately huge thank-you to preparator Kyle Davies (of apatosaur-sculpting fame), collections manager Jen Larsen, and Andrew Thomas again for help with wrassling those verts around, and for sharing their thoughts and advice. Thanks also to curators Rich Cifelli and Nick Czaplewski for their hospitality and for the go-ahead to undertake this work, and to Andy Farke for generating the model.

I’ll have a lot more to say about this stuff in the future. I didn’t go to all this work just for giggles. For a long time I’ve had a hankering to do a paper on the detailed anatomy of Sauroposeidon, based on all of the things that I’ve noticed in the last decade that didn’t make it into any of the early papers. And now there’s the proposed synonymy of Paluxysaurus with Sauroposeidon. And “Angloposeidon” needs some attention–Darren and I have been thinking about writing “Angloposeidon II” for years now. And…well, plenty more.

So, loads more to come, but not for the next few weeks. Eventually I’ll be publishing all of this–the photos, the 3D models, the whole works. Stay tuned.

UPDATE a few days later

Man, I am frazzled, because I forgot to include the moral of the story: if I can do this, you can do this. There are good, free photogrammetry programs out there–Peter Falkingham published a  whole paper on free photogrammetry in 2012, and posted a guide to an even better program, VisualSFM, on Academia.edu. Even Agisoft Photoscan is not prohibitively expensive–under $200 for an educational license. MeshLab is free and has hordes of good free tutorials. For the photography itself, you basically just build a virtual dome of photos around an object. If you need more instructions than that, Heinrich has written a whole series of tutorials. It doesn’t take a fancy camera–I used a point-and-shoot for the Sauroposeidon work shown here (a Canon S100 operating at 6 megapixels, if anyone is curious). What are you waiting for?

Sauroposeidon and friends

February 24, 2014

Sauroposeidon and kin cervicals - DRAFTAs a break from photography posts, here are four pretty big vertebrae that swirl in the same thought-space in my head. All are shown to scale, in right lateral view. These are not the biggest sauropod cervical vertebrae–Supersaurus beats them all, and there are vertebrae of Puertasaurus, Alamosaurus, and Futalognkosaurus that rival the big Sauroposeidon vert, but those are either less well preserved or still awaiting detailed description.

Incidentally, I think BYU 12867 is a C10. The centrum proportions are about right, compared to Giraffatitan, and the neural spine looks good, too, like a geometric transformation of the big Giraffatitan C8. Also, the drawn-in prezyg outline for MIWG.7306 is a little short; the actual prezyg is a monster and would have overhung the condyle by another 10cm or so. I’m pretty sure that we had a composite photograph showing this at one point, but irritatingly none of us can find it at the moment. If it turns up, I’ll update the image.

For a long time I thought Sauroposeidon was a brachiosaurid. Now it seems to be a somphospondyl (D’Emic 2012) or possibly even a basal titanosaur (Mannion et al. 2013), even if we stick just to the holotype. But if it’s not a brachiosaurid, it’s cervical vertebrae are at least coarsely brachiosaur-y in outline.

You  may recall from Naish et al. (2004) that MIWG.7306 shares several derived characters with the holotype vertebrae of Sauroposeidon. Does that mean that Angloposeidon is a somphospondyl or titanosaur as well? I dunno–as always, we need more material–but it’s an interesting possibility.

References

Weren’t we just discussing the problem of keeping up with all the good stuff on da intert00bz? The other day Rebecca Hunt-Foster, a.k.a. Dinochick, posted a “mystery photo” that is right up our alley here at SV-POW!, but, lazy sods that we are, we missed it until just now. Here’s the pic:

IMG_7857

I flipped it 90 degrees so that you can see more clearly what is going on. This is a cut and polished section of a pneumatic sauropod vertebra–the bottom half of the mid-centrum of a dorsal vertebra, to be precise. Cervicals usually have concave ventral surfaces, and sacrals are usually either wider and flatter or narrower and V-shaped in cross sections, so I am pretty confident that this slice is from a dorsal. Compare to the classic anchor cross-section in this Camarasaurus dorsal:

camarasaurus-internal-structure(You may remember this image from Xenoposeidon week–almost two years ago now!)

Naturally as soon as I saw ReBecca’s shard of excellence, I wondered about its ASP, so after a bit of GIMPing, voila:

IMG_7857 ASP

As usual, bone is black, air is white, and everything else is gray. And the ASP is:

461080 white pixels/(461080 white + 133049 black pixels) = 0.78

So, we know what this is, and we know the ASP of this bit of it, and we can even figure out the in vivo density of this bit. The density of cortical bone ranges from about 1.8  g/cm^3 for some birds to about 2.0 for most mammals. For the sake of this example–and so I can hurry back to writing my lecture about the arse–let’s call it 1.9. The density is then the fraction of bone multiplied by the density of bone, full stop. If it was an apneumatic bone, we’d have to add the fraction of marrow multiplied by the density of marrow, but the density of air is negligible so we can skip that step here. The answer is 0.22 x 1.9 = 0.42 g/cm^3, which is pretty darned light. Keep in mind, though, that some slices of Sauroposeidon (and ‘Angloposeidon’, as it turns out) have ASPs of 0.89, and thus had an in vivo density half that of the above slice (0.11 x 1.9 = 0.21 g/cm^3).

What’s that in real money? Well, your femora are roughly 60% bone and 40% marrow, with a density of ((0.6 x 2.0)+(0.4 x 0.93)) = 1.6 g/cm^3, four times as dense as the bit of vertebra shown above, and eight times as dense as some slices of Sauroposeidon and ‘Angloposeidon’. If that doesn’t make you self-conscious about your heavy thighs, I don’t know what will.

Yes, that was a lame joke, and yes, I’m going out on it.

Hat tip to Dinochick.

P.S. It’s the 40th anniversary of the first moon landing today. Hoist a brew for Neil and Buzz, wouldja?

Condrosteo_scan

By now you’ll recognize this as NHM 46870, a minor celebrity in the world of pneumatic sauropod vertebrae. Darren has covered the history of the specimen before, and in the last post he showed photographs of both this chunk and its other half. He also briefly discussed the Air Space Proportion (ASP) of the specimen, and I’ll expand on that now.

People have mentioned the weight-saving properties of sauropod vertebrae from the very earliest discoveries of sauropods. But as far as I know, no one tried to quantify just how light they might have been until 2003.

That fall I was starting my third year of PhD work at Berkeley, and I was trying to think of everything that could possibly be investigated about pneumaticity in sauropod vertebrae. I came up with a list of four things:

  • external traces of pneumaticity (foramina, fossae, tracks, laminae)
  • form and complexity of internal spaces (camerae, camellae, branching patterns)
  • ratio of bone to air space within a pneumatic element
  • distribution of postcranial skeletal pneumaticity (PSP) in the body

That list of four things formed the outline for my first dissertation chapter (Wedel 2005), and for my dissertation itself. In fact, all of my papers that have anything to do with pneumaticity can be classified into one or more of those four bins:

That list is not exhaustive. It’s every aspect of PSP that I was able to think of back in 2003, but there are lots more. For example, I’ve only ever dealt with the internal complexity of sauropod vertebrae in a qualitative fashion, but the interconnections among either chambers or bony septa could be quantified, as Andy Farke has done for the frontal sinuses of hartebeests (Farke 2007). External traces on vertebrae and the distribution of PSP in the body can also be quantified, and were shortly after I drew up the list–see Naish et al. (2004) for a simple, straightforward approach to quantifying the extent of external pneumatic fossae, and O’Connor (2004, 2009) for a quantitative approach to the extent of pneumaticity in the postcranial skeletons of birds. There are undoubtedly still more parameters waiting to be thought of and measured. All of these papers are first steps, at least as applied to pneumaticity, and our work here is really just beginning.

Also, it took me an embarrassingly long time to “discover” ASPs.  I’d had CT slices of sauropod vertebrae since January, 1998, and it took me almost six years to realize that I could use them to quantify the amount of air inside the bones. I later discovered that Currey and Alexander (1985) and Casinos and Cubo (2000) had done related but not identical work on quantifying the wall thickness of tubular bones, and I was able to translate their results into ASPs (and MSPs for marrow-filled bones).

Condrosteo_ASP

The procedure is pretty simple, as Mike has shown here before. Open up the image of interest in Photoshop (or GIMP if you’re all open-sourcey, like we are), make the bone one color, the air space a second color, and the background a third color. Count pixels, plug ’em into a simple formula, and you’ve got the ASP. I always colored the bone black, the air space white, and the background gray, so

ASP = (white pixels)/(black + white pixels)

For the image above, that’s 460442/657417 = 0.70.

Two quick technical points. First, most images are not just black, white, and one value of gray. Because of anti-aliasing, each black/white boundary is microscopically blurred by a fuzz of pixels of intermediate value. I could have used some kind of leveling threshold thing to bin those intermediate pixels into the bone/air/background columns, but I wanted to keep the process as fast and non-subjective as possible, so I didn’t. My spreadsheet has columns for black, white, gray, and everything else. The everything else typically runs 1-3%, which is not enough to make a difference at the coarse level of analysis I’m currently stuck with.

Second, I prefer transverse sections to longitudinal, because most of the internal chambers are longitudinally oriented. That means that longitudinal sections, whether sagittal or horizontal, are likely to cut through a chamber wall on its long axis, which makes the walls look unnaturally thick. For example, in the image above the median septum looks 5-10 times thicker than the outer walls of the bone, which would be a first–usually the outer walls are thicker than the internal septa, as you can see here. I don’t think the median septum really is that thick; I strongly suspect that a very thin plate of bone just happened to lie in the plane of the cut. It takes some work to get used to thinking about how a 2D slice can misrepresent 3D reality. When I first started CT scanning I was blown away by how thick the bone is below the pre- and postzygapophyses. I was thinking, “Wow, those centrozygapophyseal laminae must have been way more mechanically important than anyone thinks!” It took me a LONG time to figure out that if you take a transverse slice through a vertical plate of bone, it is going to look solid all the way up, even if that plate of bone is very thin.

Even apart from those considerations, there is still a list of caveats here as long as your arm. You may not get to choose your slice. That’s almost always true of broken or historically sectioned material, like NHM 46870. It’s even true in some cases for CT scans, because some areas don’t turn out very clearly, because of mineral inclusions, beam-hardening artifacts, or just poor preservation.

The slice you get, chosen or not, may not be representative of the ASP of the vertebra it’s from. Even if it is, other elements in the same animal may have different ASPs. Then there’s variation: intraspecific, ontogenetic, etc. So you have to treat the results with caution.

Still, there are some regularities in the data. From my own work, the mean of all ASP measurements for all sauropods is about 0.60. That was true when I had only crunched my first six images, late on the evening of October 9, 2003. It was true of the 22 measurements I had for Wedel (2005), and now that I have over a hundred measurements, it’s still true. More data is not shifting that number at all. And Woodward (2005) and Schwartz and Fritsch (2006) got very similar numbers, using different specimens.

This is cool for several reasons. It’s always nice when results are replicated–it decreases the likelihood that they’re a fluke, and in this case it suggests that although the limitations listed above are certainly real, they are not deal-killers for answering broad questions (we are at this point seeing the forest more clearly than the trees, though).

More importantly, the mean 0.60 ASP for all sauropod vertebrae is very similar to the numbers that you get from the data of Currey and Alexander (1985) and Cubo and Casinos (2000): 0.64 and 0.59, respectively. So sauropod vertebrae were about as lightly built as the pneumatic long bones of birds, on average.

Naturally, there are some deviations from average. Although I didn’t have enough data to show it in 2005, brachiosaurids tend to have higher ASPs than non-brachiosaurids. And Early Cretaceous brachiosaurids from the US and England are especially pneumatic–the mean for all of them, including Sauroposeidon, ‘Angloposeidon’, some shards of excellence from the Isle of Wight, and assorted odds and ends, is something like 0.75-0.80, higher even than Brachiosaurus. So there’s probably a combined phylogenetic/functional story in there about the highly pneumatic, hyper-long-necked brachiosaurids of the Early Cretaceous of Laurasia. Another paper waiting to be written.

Chondrosteosaurus broken face

Here’s another shard of excellence, referred to Chondrosteosaurus, NHM R96. As Mike had discussed here before, there’s no good reason to believe that it actually is Chondrosteosaurus, and the internal structure looks considerably more subdivided than in NHM 46870. This is an anterior view, and normally you’d be seeing a nice hemispherical condyle, but all of the cortical bone is gone and the internal structure is revealed. The little black traces are bone and the brownish stuff is rock matrix filling the pneumatic cavities.

Chondrosteosaurus broken face ASP

A few years ago, Mike asked me to look at that photo and guess the ASP, and then run the numbers and see how close I got. I guessed about 78%, then did the calculation, and lo and behold, the answer was 78%. So I’m pretty good at guessing ASPs.

Except I’m not, because as any of you armed with photo software can tell, that picture has 24520 black pixels and 128152 white ones, so the ASP is actually 128152/(128152+24520) = 0.84. The moral of the story is check your homework, kids! Especially if you seem to be an unnaturally good estimator.

ASP-ESP aside, I think ASP is cool and has some interesting potential at the intersection of phylogeny and biomechanics. But the method is severely limited by sample size, which is severely limited by how much of a pain in the butt preparing the images is. In most cases you can’t just play with levels or curves to get a black and white image that faithfully represents the morphology, or use the magic wand, or any of the other myriad shortcuts that modern imaging programs offer. Believe me, I’ve tried. Hard. But inevitably you get some matrix with the bone, or some bone with the matrix, and you end up spending an impossible amount of time fixing those problems (note that this is not a problem if you use perfect bones from extant animals, which is sadly not an option for sauropod workers). So almost all of my ASP images were traced by hand, which is really time-consuming. I could pile up a lot more data if I just sat around for a few weeks processing images, but every time I’ve gotten a few free weeks there has been something more important demanding my attention, and that may always be the case. Fortunately I’m not the only one doing this stuff now, and hopefully in the next few years we’ll get beyond these first few tottering steps.

Side Note: Does NHM 46870 represent a juvenile, or a dwarf?

This came up amongst the SV-POW!sketeers and we decided it should be addressed here. Darren noted that the vert at top is pretty darned small, ~23 cm for the preserved part and probably only a foot and a half long when it was complete, which is big for an animal but small for a sauropod and dinky for a brachiosaurid (if that’s what it is). Mike made the counter-observation that the internal structure is pretty complex, citing Wedel (2003b:fig. 12) and surrounding text, and suggested that it might be an adult of a small or even dwarfed taxon. And I responded:

I’m not at all certain that it is dwarfed. It matters a lot whether the complex internal structure is polycamerate or camellate. I was agnostic for a long time about how different those two conditions are, but there is an important difference that is relevant in this case: the two internal structures develop differently. Polycamerate verts really do get progressively more complex through development, as illustrated–there are at least two great series that show this, that I need to publish one of these days. But I think camellate vertebrae may be natively complex right from the get-go; i.e., instead of a big simple diverticulum pushing in from the side and making a big camera first, a bunch of smaller diverticula may remodel the small marrow spaces into small air spaces with no prior big cavities. At least, that’s how birds seem to do it. This needs more testing from sauropods–a good ontogenetic sequence from Brachiosaurus would be clutch here–but it’s my working hypothesis. In which case NHM 46870 may be a juvenile of a camellate taxon, rather than an adult of a polycamerate taxon.

The whole camerate-vs-camellate problem deserves a post of its own, and this post is already too long, so we’ll save that for another day.

References

[Disclaimer: in this post, I am unavoidably critical of certain aspects of particular journals.  Please take this in the spirit it’s intended: I’m not out to get anyone, but I need to illustrate my points with real examples.]

When we started blogging our recent neck-posture paper (Taylor et al. 2009, for those of you who’ve been chatting in the back row and not paying attention), we expected to make two posts, maybe three.  Yet here we are in post six, and I know Matt has another up the barrel for tomorrow, so it looks like we’re going to end up having written a whole week’s worth of daily posts, just as we did for Xenoposeidon.

One of the questions a lot of people have asked me is why we published in a Polish journal (Acta Palaeontologica Polonica).  Although APP is published in Poland and edited by a primarily Polish board, it’s more accurate to characterise it as an international journal — the papers in the issue where our work appeared had lead authors based in Poland (4 papers), USA (3), Italy (2), and England, France, Japan, Spain and Sweden (1 each).  Still, that question is a nice jumping-off point to discuss something of relevance to all academics that doesn’t get a lot of coverage: how to choose a journal.

From another sauropod paper in Acta Palaeontologica Polonica: Schwarz et al. (2007: fig. 1), showing CT scans of a Diplodocus cervical

From another sauropod paper in Acta Palaeontologica Polonica: Schwarz et al. (2007: fig. 1), showing CT scans of a Diplodocus cervical

Criteria for choosing a journal

There are plenty of criteria that come in to play in picking a journal, and people will vary in how much weight their place on each.  We’ll take a look at some of them (in no very convincing order), and then I’ll explain what I think is the unifying principle.

Impact factor. I’ll deal with this first, because it’s easiest to dismiss.  The impact factor is a stupid, irrelevant number attached to journals by a private corporation with its own agenda and with no responsibility to actual scientists.  Its use is particularly dumb in palaeo, a field in which it’s near impossible to get a paper written, submitted, reviewed and published in time to hit the two-year window during which citations are counted for impact-factor purposes — which is why even the best palaeo journals (JVP, Palaeontology, APP) have impact factors close to 1.0.  All scientists should ignore impact factor whenever possible.

Prestige. Now we’re getting somewhere.  Prestige is what impact factor is a (wholly inadequate) proxy for.  Of course, it’s impossible to define or quantify satisfactorily, but we all know what we mean by it.  Sadly, top of the tree for prestige — by a long way — are the “tabloids”, Science and Nature.  It’s considered a huge deal to publish in these, very good for your career — which is a shame, as the super-short format makes it nearly impossible to do decent science in these venues.  As Exhibit A, I give you Sereno et al. (1999).  In five pages, Sereno and his ten co-authors presented descriptions of not one but two new sauropod genera, plus a time-calibrated phylogeny and an analysis of rates of morphological change through time.  It is not intended as a criticism of Sereno and his colleagues when I say that for scientific purposes, the descriptions in this paper are essentially worthless — it’s simply not possible to do anything like justice to two genera, both represented by nearly complete remains, in that amount of space.  Lest I seem to be picking on this particular team, which I honestly assure you is not my purpose here, I could equally point to Curry Rogers and Forster’s (2001) description of Rapetosaurus, Rauhut et al. (2005) on Brachytrachelopan or indeed the original DinoMorph paper (Stevens and Parrish 1999).  The publication of important work in the tabloids is not such a disaster when conscientious authors such as John Hutchinson follow up a high-prestige extended abstract such as Hutchinson and Garcia (2002) with a full-length study elsewhere (Hutchinson et al. 2005), but sadly this seems to be more the exception than the rule — after all, if you’ve already got all that credit for a short paper, why bother doing all the extra work involved in getting the full-length paper done?  That said, I am assured that Curry Rogers’s long-awaited Rapetosaurus osteology is on the way RSN.  At the risk of sounding sour-grapesy (I’ve never been published in either tabloid myself), I do think that the existence of these journals is a net negative for actual science.  I won’t go so far as to say that I’ll never publish in S‘n’N if I get the chance, but I do right here and now undertake that if ever that chance should come my way, I will do my level best to get the full-length study out as soon as possible thereafter.

Hmm, that seems to have turned into a tangential rant about the tabloids, which really wasn’t my intention, but so it goes.  More generally, there is a sense that general-science journals are more prestigious than specialist palaeo journals: notable ones include PNAS and the various Royal Society journals.  An exception to this rule is the PLoS journals: because it’s more selective PLoS Biology is considered more prestigious than the general-science PLoS ONE.  Among palaeo journals, there’s a feeling that Paleobiology is particularly well regarded, with Palaeontology, the Journal of Paleontology, JVP and Acta Pal. Pol. up on its shoulders.  Other journals are a little further down the great chain of being.

How much does prestige matter?  Quite a lot (especially if you need your CV to look good) but rather less than a few years ago, I think — for reasons that will become apparent later on.

Turnaround speed. The importance of this will vary at different times.  I’ve had a couple of my papers published in PaleoBios, the journal of the University of California Museum of Paleontology — which is not particularly high-profile — for one main reason: they turn papers round really quickly.  That was particularly important to me when I was starting out, and really needed to get something on my CV quickly.  Now that my publication list is a little less feeble, I can afford to let my manuscripts marinate for longer in order to get them into more recognised journals.  But sometimes that goes to ridiculous extremes: a while back, Matt and I sent a paper to Paleobiology.  The editors sat on the manuscript for more than a month before even sending it out to reviewers.  When I asked two months later, then again a month after than, then again a month after that, reviews were still not in.  In the end, we didn’t hear back until more than six months after submission — and when we finally saw the reviews, one of them consisted only of filling in a one-page form.  We weren’t impressed, and won’t be submitting there again, despite the journal’s high prestige.  (We know others who have had even longer waits.  Sadly, we didn’t know this at the time we submitted; if we did, we’d have made other plans).

At the other end of the scale, Acta Pal. Pol. did a very fast job: just under one month elapsed after our initial submission of the neck-posture paper before we got back two detailed and helpful reviews accompanying a provisional acceptance.  It took us a fortnight to make the revisions, and only one further week for the revised manuscript to be accepted and in press — seven weeks from start to end, and then a wait of only two and a half months before publication.

Figure reproduction. This varies in importance depending on what kind of paper you’re submitting: for a description, I think it’s really important (which is why Darren and I argued, successfully, with the Palaeontology editor to get full-page reproduction for the Xenoposeidon photographs and interpretive drawings); for a biomechanics paper or similar, it’s maybe not so important, provided the figures are legible.  In terms of electronic figure reproduction, the hands-down winner is the PLoS series of journals: for example, the individual elements surrounding the skeletal reconstruction in the full-sized figure 3 of Sereno et al.’s (2007) description of the skull of Nigersaurus are exquisite.  At the other end of the scale, one of the big disappointments with Palaeontologia Electronica is the figure quality: for example, Rose’s (2007) description of Paluxysaurus has really tiny online images of the figures — something there’s no real excuse for in an online-only journal.

Length restrictions/page charges. Some journals charge the author per printed page; some charge per page after a certain number of free pages.  The charges, and the number of free pages, vary wildly between journals.  Some, maybe most, journals will waive these fees for authors with no institutional support.  Need I say that you want to find a journal that won’t charge, or will charge only a little?

(For journals that take away your copyright and restrict your use of your own work, I think that charging as well adds insult to injury.)

Reprint costs. Before the advent of ubiquitous PDFs, the main way to disseminate your work apart the journal issue itself was by buying reprints from the journal and handing them out to colleagues at conferences.  Reprint costs also very wildly between journals.  This used to be more important than it is now, as we have other ways of letting people see our work.

Wide distribution of physical issues. If your article is in Science or Nature, then a zillion copies will be printed and sent all over the world.  If you publish in The Biennial Newsletter of the South Yorkshire Lepidopterists’ Society, eight copies will be photostatted and sent as far afield as North Yorkshire.  So you might think that wide distribution correlates strongly with prestige, but that’s not always true.  A nice outlier here is PaleoBios: copies are sent to libraries all over the world, in exchange for copies of other institutional journals, which means that anything published in PaleoBios can be found in hardcopy in a surprising number of places.  This is nice; but as with reprints, less important than it was even a few years ago.  And the reason is …

Existence of PDFs. Finally we get to the bit that we’ve all known was coming.  In this enlightened day and age, most of us have several metric shedloads of papers in PDF form on our hard drives, meaning that whenever we go to a musuem with our laptops and want to compare an alleged basal titanosauriform median caudal with those of Brachiosaurus brancai, we have only to pull up the PDF of Janensch (1950) and we’re done.  Lugging around great stacks of actual paper seems not merely unnecessary but passé, like wearing flared trousers or listening to the Spice Girls.  Everyone needs PDFs, and everyone knows that this is the case.  So every publication venue provides authors with them … right?

Amazingly, no.  Things may have changed since 2007, but back then authors had to PAY $100 to the Journal of Paleontology to get a PDF of THEIR OWN PAPER.  Oh, and money orders were only accepted from the USA and Canada, so good luck if you’re a European author.  These facts hurt so much I am going to have to go and lie down before continuing.

… later … Here’s one that hurts even more: Brusatte et al.’s (2008) osteology of the stinkin’ theropod Neovenator DOES NOT EXIST as a PDF, except for a crappy scan.  Apparently the Palaeontographical Society doesn’t give the authors PDFs at all, at any price.  For me, that is a simple, non-negotiable Submission Killer: I will never, ever send my stuff to a venue that doesn’t give me a PDF.  In 2009, the idea is untenable.

Open access. Assuming that a PDF exists, who can get it and under what terms?  Under the classical model, publishers own your work, and can — and do — restrict access to it.  To see what you wrote, other scientists, and interested amateurs, have to either have an institutional subscription or pay some ludicrously inflated fee like $30.  (I wonder whether anyone in world history has ever done this?)  See Scott Aaronson’s rather brilliant article for more on this extraordinary state of affairs.

In contrast, an increasing number of journals are now open access, which means that anyone, anywhere can download the PDF with minimum fuss and at no cost.  Acta Palaeontologia Polonica is one of these, and was among the first in palaeo.  Other notable journals in this category include PLoS Biology and PLoS ONE, and Zootaxa.  If you’re prepared to wait a year before your paper becomes open access (i.e. wait until everyone who’s interested has long had a copy and all the buzz has died down so that no-one cares any more), then the list of open access journals grows to include venues like Science and Proc. B, but personally I am inclined to feel that this is stretching the definition well past breaking point.  There are good and valid reasons for wanting to publish in these venues, but their open-access-but-not-in-any-way-that-matters policy is not one of them.

There are (at least) two reasons to favour open-access journals: the pragmatic one is that it’s the best way to make sure that anyone, anywhere in the world who’s interested in your work can get it — whether professor, curator, student, interested amateur or vaguely interested high-school kid.  The other reason is that it’s just right.  We’re talking here about the world’s accumulated knowledge, in many cases acquired by publicly funded research programs.  It is simply and plainly wrong that this work should be shut up behind paywalls where the people who paid for it can’t see it.

Copyright retention. Most publishers, including some open access publishers, require the author to sign over copyright as a condition of publication.  Even if it doesn’t make much difference in practice, I have to say it rankles that, for example, that the Palaeontological Society has ended up owning my and Darren’s work on Xenoposeidon (Taylor and Naish 2007).  This is particularly iniquitous in unashamedly commercial publishers such as Elsevier — guess who owns Darren’s paper on “Angloposeidon” (Naish et al. 2004)?  And it’s even more baffling in open-access journals since they let anyone have the work anyway.  I assume the real reason for this is that publishers want to be able to exploit any spin-offs such as popular books, but copyright transfer forms usually contain a lot of blurfl about it being for the author’s benefit, as it allows the publisher to pursue infringement claims on the author’s behalf.  To which I offer the following rebuttal: “yeah, right”.

Not all publishers do this.  Notably, we retain the copyright on our recent paper in Acta Pal. Pol., Zoologica Scripta leaves copyright with the authors, and there are others.  Good for them.

… and finally, you do need to be realistic. Despite my whining about Science and Nature above, I don’t deny that we’d have loved to place the neck-posture paper at one of those journals: apart from anything else, it would be useful for Matt as he works towards tenure, and helpful for Darren who — astoundingly — is still without a job in academia.  S‘n’N papers help with that stuff.  But we know (these journals make no secret of it) that they reject 90% of submissions without even reviewing them, and it would likely just have been a waste of our time and effort to lobotomise our eight-pager down to three and reformat with the ultra-dumb numbered-references format in exchange for a tiny, tiny chance of hitting that jackpot.  So we didn’t bother.  (Also, while scientists strive to evaluate work on its merits, I can’t help suspecting that a submission to the tabloids with University of Portsmouth and Western University of Health Sciences in the byline would have started with something of a handicap in the selection process.)

What it all means

So apart from having suggested you ignore Impact Factor, I’ve said to consider prestige, reprint costs, distribution of physical issues, existence of PDFs, open access, copyright retention, turnaround speed, figure reproduction and length restrictions/page charges.  And the interesting thing is that the first half dozen of these are all about the same thing, which I’d argue is the underlying issue:

Getting the paper read by as many people as possible.

That’s what it’s really about, isn’t it?  The reason you want cheap reprints is so you can give them to people who’ll read them; the reason you want wide distribution of physical issues is so they’ll get into libraries where people will read them; and so on.

But both reprints and physical issues are much less important than they used to be, because now we can email our stuff to anyone in the world.  So let’s ignore them for now.  Prestige is less important than it used to be, because one of its big wins was that it got your article into the hands of potential readers; but it’s still important in other ways. And let’s ignore journals that don’t give you PDFs because they are off the Submission Radar.

Now here’s another thing:

Everything is open.

It just is, and there’s nothing that anyone can do about it.  Everything that becomes available as a PDF is quickly passed around the community, and in most cases posted on the author’s web-site (whatever the journal’s Arbitrary And Exploitative Copyright Transfer Form said).  So from a purely pragmatic perspective, you could say that in choosing a journal we can also ignore the criterion of whether or not the journal considers itself open access (because it really is anyway) and also copyright retention (since it doesn’t really matter if everyone can read it anyway).

So what criteria are we left with?  Of the ten we started with, those left standing in the era of ubiquitous PDFs number just four: prestige, turnaround speed, figure reproduction quality and length restrictions/page charges.  And this is excellent, because these are the actual services that journals provide to authors.  A journal best serves authors by handling their manuscripts quickly and without charge, by imparting prestige due to the reputation of the editorial board and quality of previous issues, and by reproducing the figures well.  I think it’s great that we’re moving inexorably towards an economy where the journals that get the best submissions will be the ones that provide the best services.

And among journals that do these things well, it’s fairer to reward the good guys by bestowing our submissions on those that are deliberately publishing open access rather than those that try to stop people reading what they “publish” (which, of course, is ironically the very opposite of what the word is supposed to mean, i.e. making something available).  There are some non-open journals that you sort of have to publish in — I don’t feel my CV would be complete without papers at JVP and Palaeontology — but aside from those society-owned journals (and, OK, museum journals), I am planning to pretty much stick to open access venues from here on.

In Praise of Acta Pal. Pol.

I’ll finish by mentioning that Acta Palaeontologia Polonica does offer a very good blend of the qualities we’re looking for in a publication venue: it’s open access by design (and has been for years), turnaround is very fast, the figure reproduction is good (though perhaps not stellar), and the page charges of 27 Euros per page over the first eight are not unreasonable.  (It also has cheap reprints and is widely distributed, but we’re ignoring those factors, remember?)  Finally, the journal has a well-earned reputation for publishing good papers and for reviewing them well.  So all in all, we’re really pleased with APP and would definitely use it again.

References

  • Brusatte, Stephen L., Roger B. J. Benson, and Stephen Hutt.  2008. The osteology of Neovenator salerii (Dinosauria: Theropoda) from the Wealden Group (Barremian) of the Isle of Wight.  Monograph of the Palaeontographical Society 162 (631): 1-166.
  • Curry Rogers, Kristina and Catherine A. Forster.  2001.  The last of the dinosaur titans: a new sauropod from Madagascar. Nature 412: 30-534.
  • Hutchinson, John R. and Garcia, Mariano.  2002. Tyrannosaurus was not a fast runner.  Nature 415: 1018-1021
  • Hutchinson, John R., Frank C. Anderson, Silvia S. Blemker, and Scott L. Delp.  2005.  Analysis of hindlimb muscle moment arms in Tyrannosaurus rex using a three-dimensional musculoskeletal computer model: implications for stance, gait, and speed. Paleobiology, 31(4): 676-701.
  • Janensch, W. (1950). Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3: 27-93.
  • Naish, Darren, David M. Martill, David Cooper and Kent A. Stevens.  2004.  Europe’s largest dinosaur?  A giant brachiosaurid cervical vertebra from the Wessex Formation (Early Cretaceous) of southern England.  Cretaceous Research 25: 787-795.
  • Rauhut, O. W. M., K. Remes, R. Fechner, G. Cladera, and P. Puerta. 2005.  Discovery of a short-necked sauropod dinosaur from the Late Jurassic period of Patagonia. Nature 435:670-672.
  • Rose, Peter J.  2007.  A new titanosauriform sauropod (Dinosauria: Saurischia) from the Early Cretaceous of central Texas and its phylogenetic relationships.  Palaeontologia Electronica 10 (2): 8A.
  • Schwarz, Daniela, Eberhard Frey and Christian A. Meyer.  2007. Pneumaticity and soft-tissue reconstructions in the neck of diplodocid and dicraeosaurid sauropods.  Acta Palaeontologica Polonica 52 (1): 167-188.
  • Sereno, Paul C., Allison L. Beck, Didier. B. Dutheil, Hans C. E. Larsson, Gabrielle. H. Lyon, Bourahima Moussa, Rudyard W. Sadleir, Christian A. Sidor, David J. Varricchio, Gregory P. Wilson and Jeffrey A. Wilson.  1999.  Cretaceous Sauropods from the Sahara and the Uneven Rate of Skeletal Evolution Among Dinosaurs.  Science, vol. 282, pp. 1342-1347;
  • Sereno, Paul C., Jeffrey A. Wilson, Lawrence M. Witmer, John A. Whitlock, Abdoulaye Maga, Oumarou Ide and Timothy A. Rowe.  2007. Structural Extremes in a Cretaceous Dinosaur. PLoS ONE 2 (11): e1230 (9 pages).  doi:10.1371/journal.pone.0001230
  • Stevens, K. A., and Parrish J. M., 1999, Neck Posture and Feeding Habits of Two Jurassic Sauropod Dinosaurs: Science, 284: 798-800.
  • Taylor, Michael P. and Darren Naish.  2007.  An unusual new neosauropod dinosaur from the Lower Cretaceous Hastings Beds Group of East Sussex, England.  Palaeontology 50 (6): 1547-1564.  doi: 10.1111/j.1475-4983.2007.00728.x
  • Taylor, Michael P., Mathew J. Wedel and Darren Naish.  2009.  Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2): 213-220.

Invading the postzyg

March 30, 2008

7306-fossa-medial-side-postzyg-resized.jpg

Again, another exclusive peek at an interesting specimen: the MIWG.7306 vertebra, aka ‘Angloposeidon’ (Naish et al. 2004). Apologies if, by now, you’re bored of my show-casing of this specimen, but – not only is it the only sauropod vertebra of which I personally have multiple unpublished images – it is also a really nice demonstration of the fact that, even in just a single vertebra, there are multiple interesting, bizarre, and sometimes under-studied or even un-studied details.

What we’re looking at here is the medial (‘inside’) surface of the left postzygapophysis, with the centrum down below the bottom of the image, and the cotyle off to the left (the opposite side of what’s shown here). The image below should help with orientation. The focus of interest is the unusual matrix-filled space in the middle of the image: just what is it? Because it has sharp, clean edges, I am pretty convinced that it’s natural, and I assume it’s a pneumatic foramen. Similar structures are present on the medial side of the right postzygapophysis, and are different in position and shape (Naish et al. 2003, p. 790). We think, based on several lines of evidence, that the space between the postzygapophyses (limited anteriorly by the neural spine) was occupied by an air-sac (Schwarz & Fritsch (2006) called this the interspinal diverticulum), so is this evidence that diverticula from the interspinal air-sac invaded the bodies of the postzygapophyses on their medial sides? If so, was this just a one-off in MIWG.7306, or was it widespread in brachiosaurs, in macronarians, in neosauropods, or even in sauropods as a whole? I admit that I haven’t yet taken the time to check properly, but the big problem is that this part of the vertebra – the medial surface of the postzygapophysis – is rarely figured. Based on what has been published, I have yet to see a similar structure, even in Brachiosaurus (which is very well figured, as sauropods go).

miwg7306-prezyg-fossa-composite-resized.jpg

I’m sure that someone is now going to make me look very, very silly. But, whatever. I can’t pretend to know everything. Note that, again, this is a world first. Yes, all of this stuff should be published… and in time in will, in time.

References

  • Naish, D., Martill, D. M., Cooper, D. & Stevens, K. A. 2004. Europe’s largest dinosaur? A giant brachiosaurid cervical vertebra from the Wessex Formation (Early Cretaceous) of southern England. Cretaceous Research 25, 787-795.
  • Schwarz, D. & Fritsch, G. 2006. Pneumatic structures in the cervical vertebrae of the Late Jurassic Tendaguru sauropods Brachiosaurus brancai and Dicraeosaurus. Eclogae geol. Helv. 99, 65-78.

The heart of the matter

March 12, 2008

It’s a lonely night here at the Fortress of Sauropoditude. Darren is off at one of his numerous conferences, and Mike is in hiding, trying to avoid the reality that 4% of a millennium has passed since he was loosed upon the world. I gave the serfs the night off, which means it’s just me here in this lonely tower, surrounded by arcane devices, mouldering tomes and piles of ancient bones. The candles are lit, the wine is open on the sideboard, and I am in quest of something appropriately baroque for our evening’s contemplation. How about…a vertebra with no outsides?

iow-cut-section-500.jpg

Here is a sauropod specimen with no external morphology whatsoever. This is a cut and polished section of a fragmentary vertebra from the Isle of Wight. The black lines are bony septa that make up the internal structure of the vertebra. The brownish gray stuff between the septa is matrix (rock) filling the air spaces.

How much can we infer about the animal whose mortal remains these are, in the utter absence of soft tissue or external form?

The first thing that we note is that the vertebra has a complex internal structure, one that is highly subdivided into lots of irregular cavities. Complex internal structures are present in the vertebrae of mamenchisaurs, diplodocids, and most titanosauriforms, so we know that this chunk is not from a cetiosaur or dicraeosaur or camarasaur. It is from Early Cretaceous rocks from England, so we can provisionally rule out mamenchisaurs as possible donors. Diplodocids are represented in the Early Cretaceous of England by perhaps one bone or perhaps none at all. However, titanosauriforms were all over the place in the Early Cretaceous in the Northern Hemisphere generally, and in England particularly, and on the Isle of Wight especially. So we might guess that this is a chunk of a titanosauriform.

We should also pay attention to the size of the specimen: the vertebra of which it was a part was somewhat more than 15 cm in diameter, and may have been much larger. Now, 15 cm is not huge, but it means that is not from a very small sauropod like Europasaurus. And it is another line of evidence against a dicraeosaurid or rebbachisaurid identification.

Finally, we might be curious about the ratio of bone to air space. As frequent commenter Mike From Ottawa noted of another pneumatic vertebra, “There’s almost nothing but nothing there.” In fact, the plane exposed here is about 85% space and only 15% bone, which puts it up into “Angloposeidon”-Sauroposeidon territory. Most pneumatic sauropod vertebrae were about 60% air by volume, which is remarkable enough when you stop and think about it.

So based on qualitative (complex) and quantitative (85% air) assessments of its form, and given its size and stratigraphic and geographic context, my best guess is that this is a chunk of “Angloposeidon” or a closely related brachiosaurid. I can’t rule out the possibility that it belongs to a titanosaur or a weird giant rebbachisaurid or something even more unlikely, but that’s not where the balance of the evidence points.

Which, I think, is not too bad for a skinless piece of crap shard of excellence* that most people wouldn’t look at twice.

Well, thanks for your company. Mind the stairs on your way down, and if the side door in the hall is open, walk by quickly and don’t look inside. With any luck, one of my compatriots will be back here to greet you next week.

*That’s what small chunks of sauropods are called. Honest!

Well, not Xenoposeidon, anyway

November 27, 2007

After eight consecutive posts on Xenoposeidon, I have to admit that even I am getting just a tiny bit bored of it, so I can only imagine how the rest of you feel. So now for something completely different:

BMNH 96 “Chondrosteosaurus”

You see before you a badly battered cervical vertebra, BMNH R96, which if I remember correctly is catalogued as belonging to “Chondrosteosaurus“. That genus, like so many from the Wealden, was erected on non-diagnostic material, and there is really no reason to think that R96 belongs to the same taxon as the Chondrosteosaurus type specimen BMNH R46869. It’s best regarded as Neosauropoda indet. (and, no, before you ask, we will not be naming it and promoting it as “The world’s second most amazing sauropod”).

The interesting thing about this specimen is that its condyle is completely eroded away. We’re looking at it in anterior view, right into the front of the centrum, and we can see a classic camellate pattern. The network of thin lines is bone; everything in between, now filled with matrix, used to be filled with air when the animal was alive. A while back, Matt ran the number on this photo and concluded that this vertebra was 78% air — a very high proportion even by sauropod standards, exceeded only by Sauroposeidon (the world’s third most amazing sauropod).

Of course it’s a shame that this bone is so poorly preserved; on the other hand, if it were complete, we wouldn’t be able to see the internal structure. Matt’s firmly of the opinion that bone not broken is a bone wasted, and I sometimes think that if he had his way, he’d go through the world’s sauropod collections with a sledgehammer, smashing all the vertebrae open in search of pneumaticity. (Note to collections staff: Just kidding! Har har!) It’s certainly true that more is known about the “Angloposeidon” vertebra than would be known if it weren’t snapped in two; and of course, we’d not have known about the internal structure of the Xenoposeidon vertebra were the condyle not blasted off.

Up till now, internal structure has been badly neglected in terms of informing sauropod phylogeny, despite Matt’s work on its evolution and distribution (Wedel 2003a, 2003b). The analyses of Wilson (2002) and Upchurch et al. (2004) each included just a single character for presacral bone texture in their matrices; and the Grand Unified Analysis of Harris (2006), which merged the Wilson and Upchurch matrices, discarded even this one character, as discussed in the supplementary data. That may be fair enough: we might not yet know enough about vertebral bone texture to code it well. But hopefully that will soon change, because there is a lot of information out there that’s not getting used.

References